soclassif

Command soclassif performs SO classification.

usage

ingenannot -v 2 soclassif file.fof --clustranded --clatype exon

positional arguments:

fof	File of files, <GFF/GTF>TAB<source>

optional arguments:

-h, –help	show this help message and exit
–clutype CLUTYPE	Feature type used to clusterize: [gene, cds], default=cds
–clustranded	Same strand orientation required to cluster features, default=False
–clatype CLATYPE	Feature type used to classify: [gene, cds], default=cds

inputs

File of Files (FoF) with all files to analyze. One per line such: <GFF/GTF>TAB<source>. If you want to analyze only isoforms of one file, put one line in the file.

outputs

Statistics for each category:

11661 metagenes with only one transcript, not analyzed
Classification:
N:O:O:0
N:N:O:1
N:O:N:0
N:N:N:1
O:N:O:1198
O:N:N:160
O:O:N:384
unclassified:11661
nb classified metagenes with all transcripts sharing the same CDS: 189

Categories defined by the SO such:

Class	definition
N:0:0	No transcript-pairs share any exon sequence

Class	definition
N:N:0	Some transcript-pairs share sequence, but none have common exon boundaries

Class	definition
N:0:N	Some transcript-pairs share no sequence, others have common exon boundaries

Class	definition
N:N:N	Some transcript-pairs share no sequence, others have common sequence and exon boundaries

Class	definition
0:N:0	All transcript-pairs share sequence in common, but none share exon boundaries

Class	definition
0:N:N	All transcript-pairs share sequence in common and some share exon boundaries

Class	definition
0:0:N	All transcript-pairs share some exons in common

As described above, the SO classification was originally based on exon boundaries, that could be highly problematic for de-novo annotations with poorly defined UTR parts. To avoid such problem, you can choose to perform the same classification based on CDS coordinates. In this case you will obtained less biased results. We tried to summarize the pro and cons of classification feature type in the following table.

	pros	cons
–clatype gene	complete gene structure analysis	too sensitive in case of divergent set of annotations (ex UTR, vs no-UTR)
–clatype cds	limited to coding sequence, avoid background noise due to UTRs. Usefull in case of poorly predicted UTRs.	structure inspection limited to cds

Each analyzed locus, associated with a category, is exported in the corresponding gff file.